D-I-TASSER P49915

D-I-TASSER results for P49915

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: P49915
Protein Name: GMP synthase [glutamine-hydrolyzing]
Gene Name: GMPS

Input Sequence in FASTA format

>P49915 (693 residues)
MALCNGDSKLENAGGDLKDGHHHYEGAVVILDAGAQYGKVIDRRVRELFVQSEIFPLETP
AFAIKEQGFRAIIISGGPNSVYAEDAPWFDPAIFTIGKPVLGICYGMQMMNKVFGGTVHK
KSVREDGVFNISVDNTCSLFRGLQKEEVVLLTHGDSVDKVADGFKVVARSGNIVAGIANE
SKKLYGAQFHPEVGLTENGKVILKNFLYDIAGCSGTFTVQNRELECIREIKERVGTSKVL
VLLSGGVDSTVCTALLNRALNQEQVIAVHIDNGFMRKRESQSVEEALKKLGIQVKVINAA
HSFYNGTTTLPISDEDRTPRKRISKTLNMTTSPEEKRKIIGDTFVKIANEVIGEMNLKPE
EVFLAQGTLRPDLIESASLVASGKAELIKTHHNDTELIRKLREEGKVIEPLKDFHKDEVR
ILGRELGLPEELVSRHPFPGPGLAIRVICAEEPYICKDFPETNNILKIVADFSASVKKPH
TLLQRVKACTTEEDQEKLMQITSLHSLNAFLLPIKTVGVQGDCRSYSYVCGISSKDEPDW
ESLIFLARLIPRMCHNVNRVVYIFGPPVKEPPTDVTPTFLTTGVLSTLRQADFEAHNILR
ESGYAGKISQMPVILTPLHFDRDPLQKQPSCQRSVVIRTFITSDFMTGIPATPGNEIPVE
VVLKMVTEIKKIPGISRIMYDLTSKPPGTTEWE

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P49915-D1	1-217	217		MALCNGDSKLENAGGDLKDGHHHYEGAVVILDAGAQYGKVIDRRVRELFVQSEIFPLETPAFAIKEQGFRAIIISGGPNSVYAEDAPWFDPAIFTIGKPVLGICYGMQMMNKVFGGTVHKKSVREDGVFNISVDNTCSLFRGLQKEEVVLLTHGDSVDKVADGFKVVARSGNIVAGIANESKKLYGAQFHPEVGLTENGKVILKNFLYDIAGCSGTF
2	P49915-D2	218-440	223		TVQNRELECIREIKERVGTSKVLVLLSGGVDSTVCTALLNRALNQEQVIAVHIDNGFMRKRESQSVEEALKKLGIQVKVINAAHSFYNGTTTLPISDEDRTPRKRISKTLNMTTSPEEKRKIIGDTFVKIANEVIGEMNLKPEEVFLAQGTLRPDLIESASLVASGKAELIKTHHNDTELIRKLREEGKVIEPLKDFHKDEVRILGRELGLPEELVSRHPFPG
3	P49915-D3	441-693	253		PGLAIRVICAEEPYICKDFPETNNILKIVADFSASVKKPHTLLQRVKACTTEEDQEKLMQITSLHSLNAFLLPIKTVGVQGDCRSYSYVCGISSKDEPDWESLIFLARLIPRMCHNVNRVVYIFGPPVKEPPTDVTPTFLTTGVLSTLRQADFEAHNILRESGYAGKISQMPVILTPLHFDRDPLQKQPSCQRSVVIRTFITSDFMTGIPATPGNEIPVEVVLKMVTEIKKIPGISRIMYDLTSKPPGTTEWE

Top 1 final models from D-I-TASSER

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.82

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	2vxoB	0.92	1.72	0.986	0.948	model1_2vxoB.pdb.gz
2	1gpmA	0.61	3.77	0.351	0.696	model1_1gpmA.pdb.gz
3	5tw7A	0.58	3.91	0.366	0.678	model1_5tw7A.pdb.gz
4	2ywcA	0.57	3.99	0.400	0.671	model1_2ywcA.pdb.gz
5	3tqiA	0.54	4.45	0.322	0.644	model1_3tqiA.pdb.gz
6	3uowA	0.50	5.90	0.221	0.659	model1_3uowA.pdb.gz
7	6jp9A	0.40	2.35	0.341	0.424	model1_6jp9A.pdb.gz
8	2dplA	0.39	2.06	0.365	0.406	model1_2dplA.pdb.gz
9	6ofbA	0.38	7.22	0.068	0.570	model1_6ofbA.pdb.gz
10	2pz8A	0.28	3.98	0.136	0.315	model1_2pz8A.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003824	0.99	catalytic activity
GO:0016884	0.85	carbon-nitrogen ligase activity, with glutamine as amido-N-donor
GO:0003922	0.82	GMP synthase (glutamine-hydrolyzing) activity
GO:0003921	0.82	GMP synthase activity

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0071704	1.00	organic substance metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0044763	0.99	single-organism cellular process
GO:0006807	0.99	nitrogen compound metabolic process
GO:1901564	0.98	organonitrogen compound metabolic process
GO:0044281	0.98	small molecule metabolic process
GO:0034641	0.98	cellular nitrogen compound metabolic process
GO:1901576	0.97	organic substance biosynthetic process
GO:1901360	0.97	organic cyclic compound metabolic process
GO:0046483	0.97	heterocycle metabolic process
GO:0044249	0.97	cellular biosynthetic process
GO:0006725	0.97	cellular aromatic compound metabolic process
GO:1901566	0.96	organonitrogen compound biosynthetic process
GO:0044711	0.96	single-organism biosynthetic process
GO:0044271	0.96	cellular nitrogen compound biosynthetic process
GO:1901362	0.95	organic cyclic compound biosynthetic process
GO:0018130	0.95	heterocycle biosynthetic process
GO:0019438	0.93	aromatic compound biosynthetic process
GO:0044238	0.92	primary metabolic process
GO:0006139	0.88	nucleobase-containing compound metabolic process
GO:0055086	0.86	nucleobase-containing small molecule metabolic process
GO:0072521	0.83	purine-containing compound metabolic process
GO:0034654	0.83	nucleobase-containing compound biosynthetic process
GO:0006753	0.83	nucleoside phosphate metabolic process
GO:1901293	0.82	nucleoside phosphate biosynthetic process
GO:0072522	0.82	purine-containing compound biosynthetic process
GO:0009167	0.82	purine ribonucleoside monophosphate metabolic process
GO:0009168	0.81	purine ribonucleoside monophosphate biosynthetic process
GO:0009150	0.81	purine ribonucleotide metabolic process
GO:0046037	0.80	GMP metabolic process
GO:0042455	0.80	ribonucleoside biosynthetic process
GO:0009152	0.80	purine ribonucleotide biosynthetic process
GO:0006177	0.79	GMP biosynthetic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0005829	0.97	cytosol

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

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Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2w00B	0.318	7.17	0.036	0.468	3.1.21.3	40
2	0.060	2jgdA	0.316	8.19	0.045	0.509	1.2.4.2	NA
3	0.060	3b9jI	0.102	5.37	0.021	0.131	1.17.1.4 1.17.3.2	154
4	0.060	2pdaA	0.298	8.34	0.040	0.486	1.2.7.1	40,74
5	0.060	3dlaD	0.320	6.14	0.054	0.407	6.3.5.1	77,107

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

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Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	2ckjD	0.330	8.25	0.044	0.535	0.54	FES	complex1.pdb.gz	34,35,36,38
2	0.01	2ckjB	0.322	8.44	0.042	0.525	0.52	FES	complex2.pdb.gz	33,35,38,41
3	0.01	2ckjC	0.329	8.31	0.036	0.535	0.62	FES	complex3.pdb.gz	32,33,34,36,105

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.